choroba has already pointed out that you have made a poor choice of modules. One of the problems with XML::Simple is that it is often difficult to dereference the complex data structure that it creates. That is true in your case. You have many more dereferencing mistakes than you realize. Your program gives up when it tries to execute the first one. The common theme in all your errors is your failure to take advantage of the dereferencing that has already been done. Here is a corrected version.

#!/usr/bin/env perl
use strict;
use warnings;

# use module
use XML::Simple;
use Data::Dumper;

# create object
my $xml = new XML::Simple;

# read XML file
my $xmlData = $xml->XMLin( "./xuo.xml", forcearray => 1 );


# print output
# print Dumper($data);
#print Dumper($xmlData);

my $main_target      = '';
my $target           = '';
my $sub_target       = '';
my $main_target_name = '';
my $target_name      = '';

foreach $main_target ( @{ $xmlData->{main_target} } ) {

    #$main_target_name = @{$main_target->{main_target_name}}[0] ;
    $main_target_name = $main_target->{main_target_name}[0];
    print "Main Target Name : ", $main_target_name, "\n";
    foreach $target ( @{ $main_target->{target} } ) {

        #$target_name = ${$target->{target_name}}[0] ;
        $target_name = $target->{target_name}[0];
        print "    Target Name : ", $target_name, "\n";

        #if ( exists $main_target->{target}->{sub_target} )
        if ( exists $target->{sub_target} ) {

            #foreach $sub_target ( @{ $main_target->{target}->{sub_tar
+get} } )
            foreach $sub_target ( @{ $target->{sub_target} } ) {

                #print "    Sub Target Name : ", $sub_target, "\n";
                print "    Sub Target Name : ",
                    $sub_target->{sub_target_name}[0], "\n";
            }
        }

    }
}

exit;
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OUTPUT:

Main Target Name : Instance
    Target Name : estspc_netlist
    Target Name : ibitmap
    Target Name : liberty
    Sub Target Name : nldm_liberty
    Sub Target Name : ccs_liberty
Main Target Name : Validation
    Target Name : bmval
    Sub Target Name : bmval_lvs
    Sub Target Name : bmval_sim
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